Name: rs1620976
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1620976

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:14830403 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.477544 (126401/264690, TOPMED)
C=0.464001 (64834/139728, GnomAD)
T=0.15804 (4466/28258, 14KJPN) (+ 17 more)
C=0.46160 (11240/24350, ALFA)
T=0.15949 (2673/16760, 8.3KJPN)
T=0.4586 (2937/6404, 1000G_30x)
T=0.4559 (2283/5008, 1000G)
C=0.4875 (2184/4480, Estonian)
C=0.4528 (1745/3854, ALSPAC)
C=0.4501 (1669/3708, TWINSUK)
T=0.2051 (601/2930, KOREAN)
T=0.4773 (903/1892, HapMap)
T=0.2009 (368/1832, Korea1K)
C=0.435 (434/998, GoNL)
C=0.427 (256/600, NorthernSweden)
T=0.278 (126/454, SGDP_PRJ)
C=0.250 (54/216, Qatari)
T=0.333 (70/210, Vietnamese)
T=0.30 (13/44, Siberian)
T=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ANKH : Intron Variant
Publications: 1 citation
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	24350	T=0.53840	C=0.46160
European	Sub	18126	T=0.54524	C=0.45476
African	Sub	4114	T=0.5367	C=0.4633
African Others	Sub	148	T=0.561	C=0.439
African American	Sub	3966	T=0.5358	C=0.4642
Asian	Sub	124	T=0.266	C=0.734
East Asian	Sub	96	T=0.25	C=0.75
Other Asian	Sub	28	T=0.32	C=0.68
Latin American 1	Sub	168	T=0.589	C=0.411
Latin American 2	Sub	670	T=0.431	C=0.569
South Asian	Sub	98	T=0.36	C=0.64
Other	Sub	1050	T=0.5362	C=0.4638

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.522456	C=0.477544
gnomAD - Genomes	Global	Study-wide	139728	T=0.535999	C=0.464001
gnomAD - Genomes	European	Sub	75744	T=0.55798	C=0.44202
gnomAD - Genomes	African	Sub	41792	T=0.54022	C=0.45978
gnomAD - Genomes	American	Sub	13600	T=0.46610	C=0.53390
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.5412	C=0.4588
gnomAD - Genomes	East Asian	Sub	3124	T=0.2545	C=0.7455
gnomAD - Genomes	Other	Sub	2146	T=0.5224	C=0.4776
14KJPN	JAPANESE	Study-wide	28258	T=0.15804	C=0.84196
Allele Frequency Aggregator	Total	Global	24350	T=0.53840	C=0.46160
Allele Frequency Aggregator	European	Sub	18126	T=0.54524	C=0.45476
Allele Frequency Aggregator	African	Sub	4114	T=0.5367	C=0.4633
Allele Frequency Aggregator	Other	Sub	1050	T=0.5362	C=0.4638
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.431	C=0.569
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.589	C=0.411
Allele Frequency Aggregator	Asian	Sub	124	T=0.266	C=0.734
Allele Frequency Aggregator	South Asian	Sub	98	T=0.36	C=0.64
8.3KJPN	JAPANESE	Study-wide	16760	T=0.15949	C=0.84051
1000Genomes_30x	Global	Study-wide	6404	T=0.4586	C=0.5414
1000Genomes_30x	African	Sub	1786	T=0.5554	C=0.4446
1000Genomes_30x	Europe	Sub	1266	T=0.5750	C=0.4250
1000Genomes_30x	South Asian	Sub	1202	T=0.4110	C=0.5890
1000Genomes_30x	East Asian	Sub	1170	T=0.2547	C=0.7453
1000Genomes_30x	American	Sub	980	T=0.434	C=0.566
1000Genomes	Global	Study-wide	5008	T=0.4559	C=0.5441
1000Genomes	African	Sub	1322	T=0.5598	C=0.4402
1000Genomes	East Asian	Sub	1008	T=0.2540	C=0.7460
1000Genomes	Europe	Sub	1006	T=0.5736	C=0.4264
1000Genomes	South Asian	Sub	978	T=0.417	C=0.583
1000Genomes	American	Sub	694	T=0.435	C=0.565
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5125	C=0.4875
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5472	C=0.4528
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5499	C=0.4501
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2051	A=0.0000, C=0.7949
HapMap	Global	Study-wide	1892	T=0.4773	C=0.5227
HapMap	American	Sub	770	T=0.444	C=0.556
HapMap	African	Sub	692	T=0.601	C=0.399
HapMap	Asian	Sub	254	T=0.189	C=0.811
HapMap	Europe	Sub	176	T=0.551	C=0.449
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2009	C=0.7991
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.565	C=0.435
Northern Sweden	ACPOP	Study-wide	600	T=0.573	C=0.427
SGDP_PRJ	Global	Study-wide	454	T=0.278	C=0.722
Qatari	Global	Study-wide	216	T=0.750	C=0.250
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.333	C=0.667
Siberian	Global	Study-wide	44	T=0.30	C=0.70
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	C=0.55

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 5	NC_000005.10:g.14830403T>A
GRCh38.p14 chr 5	NC_000005.10:g.14830403T>C
GRCh37.p13 chr 5	NC_000005.9:g.14830512T>A
GRCh37.p13 chr 5	NC_000005.9:g.14830512T>C
ANKH RefSeqGene (LRG_1362)	NG_008273.2:g.46383A>T
ANKH RefSeqGene (LRG_1362)	NG_008273.2:g.46383A>G

Gene: ANKH, ANKH inorganic pyrophosphate transport regulator (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANKH transcript	NM_054027.6:c.96+40949A>T	N/A	Intron Variant
ANKH transcript variant X2	XM_011514067.2:c.96+40949… XM_011514067.2:c.96+40949A>T	N/A	Intron Variant
ANKH transcript variant X1	XM_017009644.3:c.	N/A	Genic Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	T=	A	C
GRCh38.p14 chr 5	NC_000005.10:g.14830403=	NC_000005.10:g.14830403T>A	NC_000005.10:g.14830403T>C
GRCh37.p13 chr 5	NC_000005.9:g.14830512=	NC_000005.9:g.14830512T>A	NC_000005.9:g.14830512T>C
ANKH RefSeqGene (LRG_1362)	NG_008273.2:g.46383=	NG_008273.2:g.46383A>T	NG_008273.2:g.46383A>G
ANKH transcript	NM_054027.4:c.96+40949=	NM_054027.4:c.96+40949A>T	NM_054027.4:c.96+40949A>G
ANKH transcript	NM_054027.6:c.96+40949=	NM_054027.6:c.96+40949A>T	NM_054027.6:c.96+40949A>G
ANKH transcript variant X1	XM_005248324.1:c.96+40949=	XM_005248324.1:c.96+40949A>T	XM_005248324.1:c.96+40949A>G
ANKH transcript variant X2	XM_011514067.2:c.96+40949=	XM_011514067.2:c.96+40949A>T	XM_011514067.2:c.96+40949A>G

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

88 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss2436949	Nov 09, 2000 (89)
2	WI_SSAHASNP	ss14665303	Dec 05, 2003 (119)
3	SC_SNP	ss14846833	Dec 05, 2003 (119)
4	SSAHASNP	ss22348452	Apr 05, 2004 (121)
5	PERLEGEN	ss24427500	Sep 20, 2004 (123)
6	ABI	ss44667352	Mar 14, 2006 (126)
7	AFFY	ss66042448	Nov 30, 2006 (127)
8	ILLUMINA	ss75165216	Dec 06, 2007 (129)
9	HGSV	ss80982315	Dec 14, 2007 (130)
10	KRIBB_YJKIM	ss81559299	Dec 15, 2007 (130)
11	HGSV	ss86111053	Dec 14, 2007 (130)
12	BCMHGSC_JDW	ss93002261	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss98598566	Feb 04, 2009 (130)
14	BGI	ss104170571	Dec 01, 2009 (131)
15	1000GENOMES	ss108828862	Jan 23, 2009 (130)
16	1000GENOMES	ss111466915	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss116488711	Feb 14, 2009 (130)
18	ENSEMBL	ss142640651	Dec 01, 2009 (131)
19	ENSEMBL	ss142884372	Dec 01, 2009 (131)
20	GMI	ss155077386	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss162036514	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss164304558	Jul 04, 2010 (132)
23	ILLUMINA	ss172603825	Jul 04, 2010 (132)
24	BUSHMAN	ss199916829	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss206767992	Jul 04, 2010 (132)
26	1000GENOMES	ss221533684	Jul 14, 2010 (132)
27	1000GENOMES	ss232840089	Jul 14, 2010 (132)
28	1000GENOMES	ss240035302	Jul 15, 2010 (132)
29	BL	ss253249720	May 09, 2011 (134)
30	GMI	ss278180064	May 04, 2012 (137)
31	GMI	ss285124715	Apr 25, 2013 (138)
32	PJP	ss293485870	May 09, 2011 (134)
33	ILLUMINA	ss536902007	Sep 08, 2015 (146)
34	TISHKOFF	ss558225632	Apr 25, 2013 (138)
35	SSMP	ss652069499	Apr 25, 2013 (138)
36	EVA-GONL	ss981279927	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1072416047	Aug 21, 2014 (142)
38	1000GENOMES	ss1314025314	Aug 21, 2014 (142)
39	DDI	ss1430256627	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1581025172	Apr 01, 2015 (144)
41	EVA_DECODE	ss1590798127	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1612343332	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1655337365	Apr 01, 2015 (144)
44	EVA_SVP	ss1712746615	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1803110714	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1924541493	Feb 12, 2016 (147)
47	GENOMED	ss1970021457	Jul 19, 2016 (147)
48	JJLAB	ss2022869098	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2151017670	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2271630603	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2625933251	Nov 08, 2017 (151)
52	GRF	ss2706545519	Nov 08, 2017 (151)
53	GNOMAD	ss2821485257	Nov 08, 2017 (151)
54	SWEGEN	ss2996484318	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3025219209	Nov 08, 2017 (151)
56	CSHL	ss3346257215	Nov 08, 2017 (151)
57	ILLUMINA	ss3629184689	Oct 12, 2018 (152)
58	ILLUMINA	ss3638540238	Oct 12, 2018 (152)
59	ILLUMINA	ss3643487261	Oct 12, 2018 (152)
60	URBANLAB	ss3647993454	Oct 12, 2018 (152)
61	EGCUT_WGS	ss3664379883	Jul 13, 2019 (153)
62	EVA_DECODE	ss3714164076	Jul 13, 2019 (153)
63	ACPOP	ss3732115727	Jul 13, 2019 (153)
64	EVA	ss3763105582	Jul 13, 2019 (153)
65	PACBIO	ss3785033535	Jul 13, 2019 (153)
66	PACBIO	ss3790450712	Jul 13, 2019 (153)
67	PACBIO	ss3795327322	Jul 13, 2019 (153)
68	KHV_HUMAN_GENOMES	ss3806272240	Jul 13, 2019 (153)
69	EVA	ss3829110471	Apr 26, 2020 (154)
70	SGDP_PRJ	ss3861279044	Apr 26, 2020 (154)
71	KRGDB	ss3907725340	Apr 26, 2020 (154)
72	KOGIC	ss3956148843	Apr 26, 2020 (154)
73	EVA	ss4017194761	Apr 26, 2021 (155)
74	TOPMED	ss4650626781	Apr 26, 2021 (155)
75	TOMMO_GENOMICS	ss5170512177	Apr 26, 2021 (155)
76	1000G_HIGH_COVERAGE	ss5262981244	Oct 13, 2022 (156)
77	EVA	ss5355850381	Oct 13, 2022 (156)
78	HUGCELL_USP	ss5461319539	Oct 13, 2022 (156)
79	EVA	ss5507923918	Oct 13, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5546085186	Oct 13, 2022 (156)
81	SANFORD_IMAGENETICS	ss5637245923	Oct 13, 2022 (156)
82	TOMMO_GENOMICS	ss5706222497	Oct 13, 2022 (156)
83	YY_MCH	ss5806047466	Oct 13, 2022 (156)
84	EVA	ss5834561705	Oct 13, 2022 (156)
85	EVA	ss5854697945	Oct 13, 2022 (156)
86	EVA	ss5893117404	Oct 13, 2022 (156)
87	EVA	ss5965662749	Oct 13, 2022 (156)
88	EVA	ss5980281389	Oct 13, 2022 (156)
89	1000Genomes	NC_000005.9 - 14830512	Oct 12, 2018 (152)
90	1000Genomes_30x	NC_000005.10 - 14830403	Oct 13, 2022 (156)
91	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 14830512	Oct 12, 2018 (152)
92	Genetic variation in the Estonian population	NC_000005.9 - 14830512	Oct 12, 2018 (152)
93	The Danish reference pan genome	NC_000005.9 - 14830512	Apr 26, 2020 (154)
94	gnomAD - Genomes	NC_000005.10 - 14830403	Apr 26, 2021 (155)
95	Genome of the Netherlands Release 5	NC_000005.9 - 14830512	Apr 26, 2020 (154)
96	HapMap	NC_000005.10 - 14830403	Apr 26, 2020 (154)
97	KOREAN population from KRGDB	NC_000005.9 - 14830512	Apr 26, 2020 (154)
98	Korean Genome Project	NC_000005.10 - 14830403	Apr 26, 2020 (154)
99	Northern Sweden	NC_000005.9 - 14830512	Jul 13, 2019 (153)
100	Qatari	NC_000005.9 - 14830512	Apr 26, 2020 (154)
101	SGDP_PRJ	NC_000005.9 - 14830512	Apr 26, 2020 (154)
102	Siberian	NC_000005.9 - 14830512	Apr 26, 2020 (154)
103	8.3KJPN	NC_000005.9 - 14830512	Apr 26, 2021 (155)
104	14KJPN	NC_000005.10 - 14830403	Oct 13, 2022 (156)
105	TopMed	NC_000005.10 - 14830403	Apr 26, 2021 (155)
106	UK 10K study - Twins	NC_000005.9 - 14830512	Oct 12, 2018 (152)
107	A Vietnamese Genetic Variation Database	NC_000005.9 - 14830512	Jul 13, 2019 (153)
108	ALFA	NC_000005.10 - 14830403	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs17318568	Oct 07, 2004 (123)
rs57581613	May 23, 2008 (130)
rs60559480	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
14902734, ss3907725340	NC_000005.9:14830511:T:A	NC_000005.10:14830402:T:A	(self)
ss80982315, ss86111053, ss93002261, ss108828862, ss111466915, ss116488711, ss162036514, ss164304558, ss199916829, ss206767992, ss253249720, ss278180064, ss285124715, ss293485870, ss1590798127, ss1712746615, ss3643487261	NC_000005.8:14883511:T:C	NC_000005.10:14830402:T:C	(self)
25584861, 14240880, 10118131, 7190111, 6320610, 14902734, 5400592, 6583423, 13296024, 3534024, 28481484, 14240880, 3160203, ss221533684, ss232840089, ss240035302, ss536902007, ss558225632, ss652069499, ss981279927, ss1072416047, ss1314025314, ss1430256627, ss1581025172, ss1612343332, ss1655337365, ss1803110714, ss1924541493, ss1970021457, ss2022869098, ss2151017670, ss2625933251, ss2706545519, ss2821485257, ss2996484318, ss3346257215, ss3629184689, ss3638540238, ss3664379883, ss3732115727, ss3763105582, ss3785033535, ss3790450712, ss3795327322, ss3829110471, ss3861279044, ss3907725340, ss4017194761, ss5170512177, ss5355850381, ss5507923918, ss5637245923, ss5834561705, ss5965662749, ss5980281389	NC_000005.9:14830511:T:C	NC_000005.10:14830402:T:C	(self)
33611121, 180774261, 2815575, 12526844, 40059601, 488004338, 11915759407, ss2271630603, ss3025219209, ss3647993454, ss3714164076, ss3806272240, ss3956148843, ss4650626781, ss5262981244, ss5461319539, ss5546085186, ss5706222497, ss5806047466, ss5854697945, ss5893117404	NC_000005.10:14830402:T:C	NC_000005.10:14830402:T:C	(self)
ss2436949, ss24427500, ss44667352, ss66042448, ss75165216, ss81559299, ss98598566, ss104170571, ss142640651, ss142884372, ss155077386, ss172603825	NT_006576.16:14820511:T:C	NC_000005.10:14830402:T:C	(self)
ss14665303, ss14846833, ss22348452	NT_023089.13:14813249:T:C	NC_000005.10:14830402:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1620976

PMID	Title	Author	Year	Journal
24149131	Candidate gene analysis in israeli soldiers with stress fractures.	Yanovich R et al.	2012	Journal of sports science & medicine

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1620976